PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during development

PARP-1 fine-tunes gene expression to control energy balance and development by selectively repressing and activating critical genes for developmental progression.

We encourage our authors to provide original source data, particularly uncropped/-processed electrophoretic blots and spreadsheets for the main figures of the manuscript.If you would like to add source data, we would welcome one PDF/Excel-file per figure for this information.These files will be linked online as supplementary "Source Data" files.***IMPORTANT: It is Life Science Alliance policy that if requested, original data images must be made available.Failure to provide original images upon request will result in unavoidable delays in publication.Please ensure that you have access to all original microscopy and blot data images before submitting your revision.***- --------------------------------------------------------------------------Reviewer #1 (Comments to the Authors (Required)): This manuscript by Tulin and colleague is impressive.This manuscript describes the critical role of PARP in Drosophila differentiation.The differentiation process in Drosophila is very different than that of mammals.Thus the authors could rearrange the manuscript to present as a fonction of the various developmental stages of Drosophila.This is an excellent manuscript that complements well studies during mammalian development.
Reviewer #2 (Comments to the Authors (Required)): In this manuscript, Bamgbose and Tulin study the transcriptional role of PARP-1 during development in Drosophila using ChIPseq and RNAseq approaches in wild-type and Parp mutant third-instar lavae.They found that PARP-1 activate bivalent genes during development, maintaining the balance between metabolic and developmental gene expression, allowing proper progression through developmental stages.The manuscript is well writing and the results are conclusive.Some concerns should be addressed.1.-Does the transcriptional role of PARP-1 during development depend on its enzymatic activity?If the PARP-1 selective inhibitor AZD5305 inhibits PARP-1 in Drosophila, it might be interesting to explore this question.2.-How is PARP-1 recruited to the bivalent promoter?Minor comments 1.-Figure 1: The order of figures 1D and 1E should be changed.2.-The author states in the discussion that " recent evidence has shown that even cells with limited differentiation potential, such as mouse embryonic fibroblasts and T cells, exhibit a significant proportion of bivalent genes".However, T cells are a cell population with a high differentiation potential during the immune response.Consequently, this statement should be modified.Indeed, the presence of a significant proportion of bivalent genes in T cells would be associated with their high differentiation potential.
1st Authors' Response to Reviewers November 14, 2023 1 Dear reviewers of our manuscript, I hope this letter finds you well.We would like to express our gratitude for the time and effort that the two reviewers have invested in evaluating our manuscript titled "PARP-1 as a transcriptional rheostat of metabolic and bivalent genes during development."Their feedback has been instrumental in refining our study, and we have addressed each comment to ensure the revised manuscript meets the standards of Life Science Alliance.
Please find below our detailed response to the reviewers' comments.

Reviewer 1
This manuscript by Tulin and colleague is impressive.This manuscript describes the critical role of PARP in Drosophila differentiation.The differentiation process in Drosophila is very different than that of mammals.Thus the authors could rearrange the manuscript to present as a fonction of the various developmental stages of Drosophila.This is an excellent manuscript that complements well studies during mammalian development.
Response: We thank the Reviewer for his/her positive comments on our manuscript.PARP-1 mutant animals used in this study undergo developmental arrest during the larval-pupal transition.Thus, our goal was to understand PARP-1's transcriptional role during this critical stage of Drosophila development.Also, it is during this transition that PARP1's enzymatic activity is at its highest during Drosophila development (1).This is why the manuscript was written to focus on PARP-1's role at this stage instead of the different stages of Drosophila development.

General Comments
In this manuscript, Bamgbose and Tulin study the transcriptional role of PARP-1 during development in Drosophila using ChIPseq and RNAseq approaches in wild-type and Parp mutant third-instar lavae.They found that PARP-1 activate bivalent genes during development, maintaining the balance between metabolic and developmental gene expression, allowing proper progression through developmental stages.The manuscript is well writing and the results are conclusive.Some concerns should be addressed.
Response: We thank the Reviewer for their positive comments on our manuscript.We have addressed their concerns below: Major comments: 1.-Does the transcriptional role of PARP-1 during development depend on its enzymatic activity?If the PARP-1 selective inhibitor AZD5305 inhibits PARP-1 in Drosophila, it might be interesting to explore this question.
Response: In our previous studies, we have demonstrated that PARP1's ability to parylate chromatinassociated proteins, leading to chromatin relaxation, is necessary to facilitate transcription in Drosophila during development (2)(3)(4)(5).This underscores the importance of PARP1's enzymatic activity in its transcriptional regulatory functions.
Response: We thank the Reviewer for this interesting question.We believe this is beyond the scope of the manuscript.However, we have updated our discussion as follows: Previous studies in mammalian cells and C. elegans have shown that PARP-1 can recruit Polycomb members to sites of DNA damage (6), raising the question of whether PARP-1 also plays a similar role at bivalent promoters.In Drosophila third-instar larvae, PARP-1 binds to PRE/TRE motifs particularly the GAF motif at bivalent promoters (Figure 3E).Unlike in mammals, where TrxG and PcG proteins nucleate at bivalent promoters at unmethylated CpG islands (7), Drosophila lacks a methylated genome, and unmethylated genomic regions are undetectable (8).This difference suggests that transcriptional regulators like PARP-1 might bind to PRE/TRE motifs at bivalent promoters as part of the developmental regulation in Drosophila.
Given this context, it remains unclear how PARP-1 is recruited to these PRE/TRE motifs in Drosophila and whether it can recruit TrxG/PcG proteins to bivalent promoters as well.We speculate that in response to developmental cues, PARP-1 may form a complex with GAF at bivalent promoters, thereby facilitating gene activation.However, further investigation is necessary to clarify PARP-1 in the recruitment of TrxG and PcG proteins at bivalent promoters.
Minor comments 1.-Figure 1: The order of figures 1D and 1E should be changed.
Response: We thank the Reviewer for pointing this out.We have changed the order of figures 1D and 1E.
2.-The author states in the discussion that " recent evidence has shown that even cells with limited differentiation potential, such as mouse embryonic fibroblasts and T cells, exhibit a significant proportion of bivalent genes".However, T cells are a cell population with a high differentiation potential during the immune response.Consequently, this statement should be modified.Indeed, the presence of a significant proportion of bivalent genes in T cells would be associated with their high differentiation potential.Thank you for submitting your revised manuscript entitled "PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during development".We would be happy to publish your paper in Life Science Alliance pending final revisions necessary to meet our formatting guidelines.
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You can contact the journal office with any questions, contact@life-science-alliance.orgAgain, congratulations on a very nice paper.I hope you found the review process to be constructive and are pleased with how the manuscript was handled editorially.We look forward to future exciting submissions from your lab.Sincerely, Eric Sawey, PhD Executive Editor Life Science Alliance http://www.lsajournal.org Science Alliance Manuscript #LSA-2023-02369-TR Prof. Alexei Tulin University of North Dakota 501 North Columbia Road, Stop 90 GRAND FORKS, ND 582028367 Dear Dr. Tulin, Fig 4B, Fig S1A,B, Fig S4A,B,C,D to your main manuscript text If you are planning a press release on your work, please inform us immediately to allow informing our production team and scheduling a release date.
Thank you for submitting your Research Article entitled "PARP-1 is a transcriptional rheostat of metabolic and bivalent genes during development".It is a pleasure to let you know that your manuscript is now accepted for publication in Life Science Alliance.Congratulations on this interesting work.